Skip to content

Feature/subset pos #25

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
bobverity merged 2 commits into from
Dec 2, 2025
Merged

Feature/subset pos #25

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
cedbba8
bugfix in subset_position - causing duplication when applied to hets
bobverity Dec 2, 2025
ce13c78
updated version num
bobverity Dec 2, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion DESCRIPTION
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Package: variantstring
Type: Package
Title: Functions for working with variant string format
Version: 1.8.4
Version: 1.8.5
Authors@R: c(
person("Bob", "Verity", email = "r.verity@imperial.ac.uk", role = c("aut", "cre"))
)
Expand Down
9 changes: 6 additions & 3 deletions R/main.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -859,11 +859,14 @@ subset_position <- function(position_string, variant_strings) {
v_unique <- unique(variant_strings)

l_unique <- mapply(function(x) {
df_join <- inner_join(df_position, x, by = c("gene", "pos"))
if (nrow(df_join) == 0) {

df_intersect <- x |>
filter(gene %in% df_position$gene) |>
filter(pos %in% df_position$pos)
if (nrow(df_intersect) == 0) {
ret <- NA
} else {
ret <- long_to_variant(list(df_join))
ret <- long_to_variant(list(df_intersect))
}
ret
}, variant_to_long(v_unique), SIMPLIFY = FALSE) |>
Expand Down
2 changes: 1 addition & 1 deletion README.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ Tools for working with *variant string format*, a convenient format for encoding
You can install directly from Github:

```{r, eval=FALSE}
devtools::install_github(repo = "mrc-ide/variantstring@v1.8.4")
devtools::install_github(repo = "mrc-ide/variantstring@v1.8.5")
```

Note the use of the @ symbol to reference a specific tagged version. This is highly recommended as the package is still in development and backwards compatibility is not guaranteed.
Expand Down
2 changes: 1 addition & 1 deletion README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ other.
You can install directly from Github:

``` r
devtools::install_github(repo = "mrc-ide/variantstring@v1.8.4")
devtools::install_github(repo = "mrc-ide/variantstring@v1.8.5")
```

Note the use of the @ symbol to reference a specific tagged version.
Expand Down